For clarification, when you say "account" which product are referring to? For non-profits we only offer server licenses for products like JIRA, Confluence, Bamboo, Crowd. However, we do offer free non-profit accounts for Bitbucket Cloud and HipChat Cloud, but not for the Cloud versions of JIRA, Confluence, etc.
In the application, it does state a free Bitbucket Cloud account must be created first (same for HipChat Cloud), and we will convert it to a Community (non-profit) account once the application is processed and meets the requirements for Community (non-profit) status.
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When you apply for an Atlassian Community License we ask for up to two weeks for the application to be processed, but it is generally processed much quicker when the non-profit documentation is comprehensive. When the application is approved we issue the community server license(s) to a my.atlassian.com account and provide instructions on how to retrieve the server license(s).
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